@reporter: Can you, please, try the development version of NetBeans [1]? If you can reproduce, can you please tell us what is your Initial Directory [2] and Upload Directory [3]?
@Láďa: Can you please try to reproduce this issue?
Thanks a lot.

This bug happens only for "/" as a base remote directory.
Should be fixed now, Láďo, please verify [1] so I can backport it to NB 7.1 branch.
http://hg.netbeans.org/web-main/rev/e40d004698b4
Thanks.
[1] Please, verify both, "/" as well as "/mydir" base remote directories.

The reported error still persists, even when using the nightly build of Netbeans 7.2, which is currently 201205300001.
I have attached the output of Netbeans to this bug report. There you can see the problem at the end of the file:
"CWD /var/kunden/webs/blaudirekt/portal/vermittler/unde" -> this is faulty, as it should be
"CWD /var/kunden/webs/blaudirekt/portal/vermittler/kunde".
If you need additional information please let me know.

I have uploaded screenshots for [1] and [2].
Basic environment: I have a webspace on a server which is accessed via sftp in Netbeans. Those files are mirrored on my computer. The Netbeans-project refers to the files on my computer and is ordered to update the files on my webspace on save-command.
As for the reproduceability:
- make a change in a file
- save the file (Netbeans is supposed to upload the file to the server)